LAMMPS (7 Aug 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Nose-Hoover)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style fourier
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
  5 = max # of 1-2 neighbors
  10 = max # of 1-3 neighbors
  16 = max # of 1-4 neighbors
  20 = max # of special neighbors
  special bonds CPU = 0.0019815 secs
  read_data CPU = 0.0168803 secs

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT


neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
  1250 = # of size 2 clusters
  0 = # of size 3 clusters
  250 = # of size 4 clusters
  0 = # of frozen angles
  find clusters CPU = 0.000715256 secs

compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude

fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 260 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 1 20.0
fix fINVERSE all drude/transform/inverse

fix fMOMENTUM all momentum 100 linear 1 1 1

thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
  G vector (1/distance) = 0.382011
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0325934
  estimated relative force accuracy = 9.8154e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 103823 64000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
      50    3563.3755    4630.6343    321.47655   -1067.2588    735.72049    604.78665    689.14827    -3277.411    815.58183    1306088.7   -1306723.8    17813.424    48631.318      503.827 0.0087118192 
     100    3327.4724    4395.1107    305.12559   -1067.6382    597.93176    651.62645     945.4151   -3267.2851    584.58833    1306135.9   -1306715.8    17407.337    48631.318    478.20171 0.0075985539 
     150    3036.9065    4740.2304    329.08513   -1703.3239    558.64983    619.91284    658.80687   -3278.7837    285.12462      1306173     -1306720    18448.248    48631.318    515.75286 0.0063215188 
     200     2697.958    4559.3445    316.52733   -1861.3864    522.09334    593.89129    754.61446     -3273.49    87.660461    1306183.9     -1306730    17888.936    48631.318    496.07143 0.0068706164 
     250    2348.7568     4410.585    306.19988   -2061.8283    506.05007    575.35171    715.55054   -3276.3261   -18.364473    1306177.3   -1306741.4     11592.05    48631.318    479.88562 0.0071741032 
     300    2019.8258    4040.1415    280.48226   -2020.3157     604.3077    641.66689    693.93801   -3278.5312   -115.73641    1306183.2   -1306749.1    3631.3628    48631.318    439.57995 0.0069886387 
     350    1699.5166    3944.9851    273.87613   -2245.4685    452.07416     638.0653    658.79117   -3279.6053   -157.07584    1306196.9   -1306754.6    13544.368    48631.318    429.22694 0.0062868111 
     400    1399.2929     3726.098    258.68014   -2326.8051    457.91943    621.44726    639.39903   -3279.2395   -188.85914    1306185.4   -1306762.8    10792.274    48631.318    405.41134 0.0059340078 
     450    1120.5249     3518.345    244.25712   -2397.8201    519.48856    584.65789    646.36689   -3278.6685   -289.59913    1306184.1   -1306764.2    2755.5598    48631.318    382.80716 0.0055707485 
     500     868.0166    3359.8794    233.25583   -2491.8628     460.7393    581.49563    581.01731   -3281.5544   -252.20169    1306184.3   -1306765.7    6120.3639    48631.318    365.56528 0.0058756154 
     550    637.01567    3214.9521    223.19441   -2577.9364    431.81483    578.87411    540.94047   -3281.5337   -266.36075    1306182.8   -1306764.5    8622.4334    48631.318    349.79661 0.0058589653 
     600    418.04086    3113.4064    216.14472   -2695.3655    430.45935    538.68157    522.24598    -3283.456   -311.87901    1306174.3   -1306765.8    7068.9273    48631.318    338.74797 0.0059567598 
     650     218.5966    2930.8439    203.47052   -2712.2473    514.47294    514.28379    551.52551   -3282.0904   -405.37401    1306164.5   -1306769.5   -13.553736    48631.318    318.88482 0.0052667842 
     700     45.22721    2830.1443    196.47956    -2784.917    451.11156    498.26423    541.18835   -3282.1427   -375.95313    1306157.1   -1306774.4    3947.6276    48631.318    307.92741 0.0068019029 
     750   -114.28621    2798.3153    194.26988   -2912.6016      412.753     503.2878    481.32173   -3284.3411   -393.53984      1306147   -1306779.1    7143.3414    48631.318    304.46466 0.0061596717 
     800   -263.63817    2694.8084    187.08403   -2958.4466    455.67914    487.49754     476.8659   -3284.3133    -451.9578      1306145   -1306787.2    1185.9502    48631.318    293.20288 0.0058203332 
     850   -397.71592    2559.1921    177.66902   -2956.9081    458.83317     481.2262    478.31241    -3284.068   -437.26503    1306138.6   -1306792.6    346.80209    48631.318    278.44745 0.0054921692 
     900    -515.1823    2544.8753    176.67509   -3060.0576    395.00163    457.58988    446.68352    -3285.485   -423.56221      1306145   -1306795.3    3712.8598    48631.318    276.88864 0.0074054008 
     950   -617.28259    2451.1723    170.16987   -3068.4549    383.64277    446.59877     434.4624   -3285.1348   -391.59344    1306142.3   -1306798.7    5429.2488    48631.318    266.69431 0.0057487316 
    1000   -703.15534     2334.837    162.09342   -3037.9923    424.34948    462.21112    451.80809   -3284.3803   -426.53369    1306133.9   -1306799.3    1137.6145    48631.318    254.03675 0.0053914731 
    1050    -771.1763     2303.837    159.94128   -3075.0133    426.21409    436.50718    435.09987   -3285.1939   -411.14054    1306125.6   -1306802.1    1636.9383    48631.318    250.66295 0.0069342505 
    1100   -822.72236    2283.4196    158.52382    -3106.142    376.67684    447.77729    418.45768   -3286.5919   -377.48204    1306118.9   -1306803.8    4760.5163    48631.318    248.44119 0.0074025012 
    1150   -857.06075    2259.0717     156.8335   -3116.1324    400.31523    431.65981    457.68066   -3285.1977   -430.47723    1306115.8   -1306805.9    3194.5161    48631.318    245.79223  0.007063589 
    1200   -875.50848    2238.2637    155.38893   -3113.7722    445.38524    460.97125    432.10511   -3285.4238   -472.46606    1306114.7     -1306809   -653.49784    48631.318    243.52819 0.0071448738 
    1250   -880.37572    2294.6889    159.30618   -3175.0646    411.35427    444.73793    420.06468   -3286.0366   -458.05371    1306104.4   -1306811.5    945.80793    48631.318    249.66481  0.011853487 
    1300   -871.31064    2284.2298    158.58007   -3155.5405    404.97412    441.75285    426.34477   -3285.4859   -424.79609    1306094.9   -1306813.2    4406.6196    48631.318    248.48563  0.084424118 
    1350   -816.70005    2325.9264    161.47481   -3142.6265    696.80296    442.50053    431.19923   -3285.7859    -450.2699    1305836.2   -1306813.3     593.8098    48631.318    251.40749    2.9297319 
    1400   -794.25335    2263.5101    157.14163   -3057.7635    645.65165    466.22086    446.22268   -3285.1821   -420.65317    1305903.7   -1306813.8    1386.3633    48631.318    245.20554    1.8916154 
    1450   -776.10866    2287.6575    158.81803   -3063.7661    427.03477    479.10627    439.67495   -3285.9537   -395.13186    1306087.6   -1306816.1    2936.7806    48631.318    248.87167  0.061343245 
    1500   -725.48181     2371.413    164.63266   -3096.8948    390.03204    464.30903    446.91959   -3284.7809   -393.16613    1306095.4   -1306815.6      3544.25    48631.318    258.01286  0.011586563 
    1550    -671.4904    2315.9297     160.7808   -2987.4201    457.04935    500.25282    464.76203   -3284.9311   -400.98103    1306091.7   -1306815.3    2052.6339    48631.318    251.97726 0.0094517862 
    1600   -618.83633    2449.0918    170.02543   -3067.9281    425.47487    474.65876    471.99171   -3284.3677   -430.32107    1306091.3   -1306816.6    441.15682    48631.318    266.46311  0.014260935 
    1650   -567.82245    2425.2238    168.36842   -2993.0462    421.01953    511.27133    463.22065    -3285.038   -377.24066    1306088.4   -1306814.7    5198.8565    48631.318    263.83185  0.074738268 
    1700    -502.4486    2441.8554    169.52305    -2944.304    642.39962    512.90234    490.38297   -3283.9751   -417.39288    1305929.1   -1306817.7    1141.4411    48631.318    264.52393     2.043674 
    1750   -459.52196    2499.0746    173.49543   -2958.5966    679.38259    505.31787    484.77659   -3284.6272   -384.27736    1305861.6   -1306820.8    1527.2046    48631.318    270.10074    3.1869342 
    1800   -471.14403    2476.2266    171.90923   -2947.3706    442.47741    530.45656    474.03057   -3284.0954   -371.95117    1306084.3   -1306822.6    3392.2533    48631.318    269.36446   0.10416401 
    1850   -462.80763    2536.7112    176.10831   -2999.5188    437.08241    525.07462     474.0838   -3283.7906   -422.23719    1306091.6   -1306821.3    1629.8629    48631.318    275.99502  0.016806806 
    1900   -469.89289    2468.9765     171.4059   -2938.8694    446.77624    531.61059    496.01046   -3284.2338   -395.15325    1306085.7   -1306819.6    3119.5402    48631.318    268.62645  0.014601992 
    1950   -491.08007    2445.5966    169.78278   -2936.6767    457.80452    527.23373    470.18125   -3283.9608   -391.86377    1306101.9     -1306818    1122.5275    48631.318    266.08018  0.018911601 
    2000   -518.40811    2418.7208    167.91696   -2937.1289    415.93135     536.5973    480.44651   -3283.7881   -363.72783    1306096.2   -1306818.7    4475.7317    48631.318    263.09007   0.13504326 
Loop time of 70.696 on 1 procs for 2000 steps with 5500 atoms

Performance: 1.222 ns/day, 19.638 hours/ns, 28.290 timesteps/s
97.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 48.367     | 48.367     | 48.367     |   0.0 | 68.42
Bond    | 2.9191     | 2.9191     | 2.9191     |   0.0 |  4.13
Kspace  | 14.266     | 14.266     | 14.266     |   0.0 | 20.18
Neigh   | 1.5262     | 1.5262     | 1.5262     |   0.0 |  2.16
Comm    | 0.27841    | 0.27841    | 0.27841    |   0.0 |  0.39
Output  | 0.0035572  | 0.0035572  | 0.0035572  |   0.0 |  0.01
Modify  | 3.2856     | 3.2856     | 3.2856     |   0.0 |  4.65
Other   |            | 0.05018    |            |       |  0.07

Nlocal:    5500 ave 5500 max 5500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    15317 ave 15317 max 15317 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1.30285e+06 ave 1.30285e+06 max 1.30285e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1302849
Ave neighs/atom = 236.882
Ave special neighs/atom = 15.6364
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:01:10
